Question regarding X99 PCI-E with 5820K

the only way I can run the gpu at 16x is to use the first PCI-E slot, using any other PCI-E slot will make the GPU runs at 8x
I'm trying to use the third PCI-E but it will report 8x even if no other PCI-E cards are used.
The reason I can't use the first slot, is the space between the cooler and the GPU is too narrow.
I understand the difference between 8x and 16x is negligible but why not running at 16x even if I'm using full lanes on the CPU.

the only way I can run the gpu at 16x is to use the first PCI-E slot, using any other PCI-E slot will make the GPU runs at 8x
I'm trying to use the third PCI-E but it will report 8x even if no other PCI-E cards are used.
The reason I can't use the first slot, is the space between the cooler and the GPU is too narrow.
I understand the difference between 8x and 16x is negligible but why not running at 16x even if I'm using full lanes on the CPU.

Because thats simply how some boards are designed / run. it is different for every board.